[gmx-users] Unnatural amino acids- modifying topology files
Hello GROMACS people, I'm trying to model a protein containing the unnatural amino acid para-fluorophenylalanine (FPhe). I modified the aminoacid.dat file, as well as the .hdb and .rtp files by adapting the existing entry for PHE. I have been able to use 'grompp' and perform a minimization of an FPhe-containing protein. However when I perform 'grompp' I get a warning: WARNING 1 [file 1U70_F.itp, line 27460]: No default Proper Dih. types, using zeroes The line in the .itp file corresponds to atoms which include the CE1, CE2, CZ and F atoms of FPhe. I'm surprised that GROMACS is giving me a warning because the FPh entry in the .rtp file nearly identical to that for the PHE- the HZ atom is simply replaced by an F atom (the FPhe entry in the .rtp file is included at the end of this message). How can I rectify this situation? Thanks, Vanessa [ FPh ] [ atoms ] N amber99_34 -0.41570 1 H amber99_17 0.27190 2 CA amber99_11 -0.00240 3 HA amber99_19 0.09780 4 CB amber99_11 -0.03430 5 HB1 amber99_18 0.02950 6 HB2 amber99_18 0.02950 7 CG amber99_3 0.01180 8 CD1 amber99_3 -0.12560 9 HD1 amber99_22 0.13300 10 CE1 amber99_3 -0.17040 11 HE1 amber99_22 0.14300 12 CZ amber99_3 -0.10720 13 F amber99_16 -0.21700 14 CE2 amber99_3 -0.17040 15 HE2 amber99_22 0.14300 16 CD2 amber99_3 -0.12560 17 HD2 amber99_22 0.13300 18 C amber99_2 0.59730 19 O amber99_41 -0.56790 20 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ CZ F CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C O -C N [ dihedrals ] CA C +N +H backbone_prop_1 O C +N +H backbone_prop_2 -C N CA CB backbone_prop_3 -C N CA C backbone_prop_4 CA C +N +CA backbone_prop_1 O C +N +CA backbone_prop_1 CB CG CD1 HD1 aromatic_prop_1 CB CG CD2 HD2 aromatic_prop_1 CB CG CD1 CE1 aromatic_prop_1 CB CG CD2 CE2 aromatic_prop_1 CG CD1 CE1 HE1 aromatic_prop_1 CG CD2 CE2 HE2 aromatic_prop_1 CG CD1 CE1 CZ aromatic_prop_1 CG CD2 CE2 CZ aromatic_prop_1 CD1 CE1 CZ F aromatic_prop_1 CD1 CE1 CZ CE2 aromatic_prop_1 CD2 CE2 CZ F aromatic_prop_1 CD2 CE2 CZ CE1 aromatic_prop_1 CE1 CZ CE2 HE2 aromatic_prop_1 CE2 CZ CE1 HE1 aromatic_prop_1 HD1 CD1 CE1 HE1 aromatic_prop_1 HD2 CD2 CE2 HE2 aromatic_prop_1 HE1 CE1 CZ F aromatic_prop_1 HE2 CE2 CZ F aromatic_prop_1 HD1 CD1 CE1 CZ aromatic_prop_1 HD2 CD2 CE2 CZ aromatic_prop_1 HD1 CD1 CG CD2 aromatic_prop_1 CD1 CG CD2 HD2 aromatic_prop_1 CE1 CD1 CG CD2 aromatic_prop_1 CD1 CG CD2 CE2 aromatic_prop_1 [ impropers ] -C CA N H CA +N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2 CZ F CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using g_dih: Fatal error: Dihedral around 19, 21 not found in topology
Hi All, I would like to plot dihedral angles of a protein over a trajectory, but I can't seem to get any of the analysis programs to work for me. For example, g_dih -f confout_mod.pdb Reading file topol.tpr, VERSION 3.1.4 (single precision) Found 314 phi-psi combinations Fatal error: Dihedral around 19,21 not found in topology Alternatively, when I run g_angle I get the following error: g_angle -f confout.gro -n h_arl2.ndx -of Fatal error: number of index elements not multiple of 3, these can not be angle tripletswhen I run g_dih I suspect that there are two reasons why these programs aren't working for me: (1) I'm using AMBER force field (ffamber99) ports for GROMACS (http://folding.stanford.edu/ffamber/) so the residue names and hydrogen atom names are not the same as for other FF typically used for GROMACS. However, even when I change the residue names and remove all hydrogens to be consistent with standard GROMACS FF, I still get exactly the same error as before when using the 'g_dih' program. ( I verified that the residue and atom names were consistent with other GROMACS FF by using pdb2gmx on the modified PDB file.) (2) I don't run 'g_dih' or 'g-angle' on a trajectory, but rather on a PDB file that represents a single snapshot corresponding to the simulation output (confout.gro). I have run 'g_dih' on a trajectory (.trr) file, but I get the same error as above. I would prefer to use these programs on a trajectory, but I'm afraid that the use of a non-standard FF (and corresponding atypical residue and H atom names) precludes me from doing this. Does anybody know of a way around this? Thanks, Vanessa ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] units for Leonard-Jones parameters in gromacs topology file
Hi All, A simple question: What are the units for the Leonard-Jones potential parameters rand epsilon in the gromacs topology files. Thanks, Vanessa ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS warning
Hi everyone, I'm having trouble with performing 1 ns simulations on a 318 residue long protein with 'mdrun'. The run.log file, included at the end of this message, gives a 'LINCS warning' within a minute or two after the simulation begins: Step 148, time 0.296 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.151505 (between atoms 4353 and 4355) rms 0.002175 bonds that rotated more than 60 degrees: I've have been minimizing the structure of the protein prior to trying to perform the simulation (no problems here). Also, when I use 'grompp' to produce a .tpr file for a 1 ns MD simulation with the minimized structure, I have no problems with this either. The .mdp file that is fed into the .tpr file will work with different protein structures (single residue mutants) without incident. So, it would appear that the .mdp file used to compile the .tpr file is working. What is really puzzling to me is that the simulation will sometimes run properly and sometimes it won't even though it would appear that I use the exact same .gro file. Does this sound familiar to anyone? Thanks, Vanessa Reading file 1_T114A_F.tpr, VERSION 3.1.4 (single precision) Reading file 1_T114A_F.tpr, VERSION 3.1.4 (single precision) starting mdrun 'hALDR2 (060425 pH=6.5) w/ F inhibitor implicit water' 50 steps, 1000.0 ps. Step 148, time 0.296 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.151505 (between atoms 4353 and 4355) rms 0.002175 bonds that rotated more than 60 degrees: bonds that rotated more than 60 degrees: atom 1 atom 2 angle previous, current, constraint length 4353 4355 90.30.1010 0.1163 0.1010 Step 148, time 0.296 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.150984 (between atoms 4353 and 4355) rms 0.002227 bonds that rotated more than 60 degrees: atom 1 atom 2 angle previous, current, constraint length 4353 4355 90.00.1010 0.1162 0.1010 Step 149, time 0.298 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.053408 (between atoms 4353 and 4355) rms 0.000836 bonds that rotated more than 60 degrees: atom 1 atom 2 angle previous, current, constraint length 4353 4355 89.60.1162 0.1064 0.1010 Step 149, time 0.298 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.049700 (between atoms 4353 and 4355) rms 0.000769 bonds that rotated more than 60 degrees: atom 1 atom 2 angle previous, current, constraint length atom 1 atom 2 angle previous, current, constraint length 4353 4355 90.00.1162 0.1060 0.1010 Step 150, time 0.3 (ps) LINCS WARNING relative constraint deviation after LINCS: max 166995.593750 (between atoms 4348 and 4350) rms 3256.995850 bonds that rotated more than 60 degrees: atom 1 atom 2 angle previous, current, constraint length 4329 4331 65.30.1449 2.0483 0.1449 4331 4332 75.60.1090 2.0105 0.1090 4331 4333 64.60.1526 2.0440 0.1526 4331 4342 68.60.1522 9.4604 0.1522 4342 4343 68.40.1229 9.5175 0.1229 4342 4344 74.80.1335 33.8721 0.1335 4344 4345 79.40.1010 31.1369 0.1010 4344 4346 85.90.1450 170.9566 0.1449 4346 4347 86.50.1090 151.5872 0.1090 4346 4348 88.90.1527 774.3875 0.1526 4346 4356 84.60.1523 164.2752 0.1522 4348 4349 89.50.1091 647.3028 0.1090 4348 4350 90.00.1092 18202.6279 0.1090 4348 4351 89.70.1527 957.9619 0.1522 4351 4352 89.60.1234 262.4561 0.1229 4351 4352 89.60.1234 262.4561 0.1229 4351 4353 90.50.1355 1149.1741 0.1335 4353 4354 89.70.1007 178.1642 0.1010 4353 4355 90.00.1060 16749.2714 0.1010 4356 4357 76.10.1229 38.4753 0.1229 4356 4358 73.10.1335 39.2402 0.1335 4358 4359 69.50.1010 9.6261 0.1010 4358 4360 69.70.1449 10.2906 0.1449 4360 4361 72.90.1090 2.6064 0.1090 4360 4362 69.10.1526 2.6707 0.1526 4360 4376 63.90.1522 2.6586 0.1522 Wrote pdb files with previous and current coordinates Step 150, time 0.3 (ps) LINCS WARNING relative constraint deviation after LINCS: max 166882.437500 (between atoms 4348 and 4350) rms 3256.037109 bonds that rotated more than 60 degrees: atom 1 atom 2 angle previous, current, constraint length 4319 4321 77.00.1449 0.2666 0.1449 4321 4322 78.40.1090 0.1816 0.1090 4321 4323 72.40.1526 0.2694 0.1526 4321 4327 69.10.1522 0.3681 0.1522 4327 4328 73.50.1229 0.4389 0.1229 4327 4328 73.50.1229 0.4389 0.1229 4327 4329 80.00.1335 1.6753 0.1335 4329 4330 80.90.1010 1.3435 0.1010
[gmx-users] Parameters for unnatural amino acid F-Phe
Hi, I am trying to model a protein that contains 4-fluoro-phenylalanine. I've generated an entirely new set of parameters (using the Generalized Atom Force Field) to use in gromacs. I understand that I need to modify the .rtp file and aminoacid.dat files in order to obtain a .top file for the pdb structure (pdb2gmx). However it isn't clear to me whether I should modify the ff_bonded.itp or ff_non_bonded.itp files with my new parameters? Alternatively, I could simply use the old force field parameters (in my case ffamber99) and simply change the para H to an F atom. Would I do this modification for both the .rtp and ffamber_bonded.itp files only? Any ideas would be helpful. Thanks, Vanessa ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems during make : undefined reference to `__ctype_b'
Hi All, I'm trying to install gromacs-3.1.4 onto a linux cluster with Red Hat v 7.3. After executing 'make' i get the following printed to the screen: : undefined reference to `__ctype_b' /home/voklejas/fftw/lib/libsfftw.a(wisdom.o)(.text+0x41b): In function `read_int': : undefined reference to `__ctype_b' /home/voklejas/fftw/lib/libsfftw.a(wisdom.o)(.text+0x481): In function `read_int': : undefined reference to `__ctype_b' /home/voklejas/fftw/lib/libsfftw.a(wisdom.o)(.text+0x511): In function `fftw_import_wisdom': : undefined reference to `__ctype_b' /home/voklejas/fftw/lib/libsfftw.a(wisdom.o)(.text+0x559): more undefined references to `__ctype_b' follow collect2: ld returned 1 exit status make[3]: *** [mdrun] Error 1 make[3]: Leaving directory `/home/voklejas/gromacs-3.1.4/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/voklejas/gromacs-3.1.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/voklejas/gromacs-3.1.4/src' make: *** [all-recursive] Error 1 Any ideas as to what is causing this? Thanks, Vanessa ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] compiling gromacs with cygwin
Hi All, I want to get gromacs v 3.1.0 running on my PC via cygwin. I have been able to compile fftw-3.0.1 but, when I try to execute the configure file, it terminates when it tries (unsuccessfully) to find the fftw library. Anyone have experience with this? Thanks, Vanessa ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
